# Effect of Counterions on the Soft Ionization Mass Spectra of Analytes with Multiple Permanent Charges

## TL;DR

This paper shows how counterions affect mass spectra of multiply charged molecules, and how choosing the right counterions can improve results.

## Contribution

The study reveals how counterion-analyte interactions influence soft ionization mass spectra and introduces a combinatorial model to explain these effects.

## Key findings

- MALDI and ESI mass spectra of MPCAs are strongly influenced by counterion basicity.
- Optimal counterions like ClO4– and TfO– produce high-quality spectra for certain MPCAs.
- A combinatorial model explains how counterion binding strength affects mass spectral quality.

## Abstract

Multiply permanently charged analytes (MPCAs) are of
great interest
for various applications. MPCA soft ionization mass spectra (MS) strongly
depend on the counterions of MPCA. We have studied thoroughly this
effect to expand the use of MS in MPCA characterization. To this end,
β-cyclodextrin-based MPCAs with 7 (MIM7NBCD) and 14 (MIM14BCD)
quaternary ammonium charges with a series of monovalent counterions
were prepared and their MS were measured using two of the most popular
soft ionization techniques, electrospray ionization (ESI) and matrix-assisted
laser desorption ionization (MALDI). MALDI MS of both analytes were
well resolved, with signals assignable to the analytes only with the
two least basic tested counterions (ClO4– and TfO–). Similarly, analyte-assignable signals
were observed in ESI MS of MIM14BCD only with ClO4– and TfO–. The situation was opposite
with ESI MS of MIM7NBCD where assignable signals were observed with
Cl– but not with TfO–. Thus, to
get high-quality MS, binding between the MPCA permanent charges and
the counterions must be of the optimal effective strength, given also
by the number of analyte permanent charges as shown by the simple
combinatorial model of binding. Of practical interest is the observation
that unsuitable counterions can be replaced in situ by an excess of corresponding acid. The findings form a coherent
framework for interpreting and improving MPCA mass spectra.